We used fluorescence DNA in situ hybridization (FISH) to detect chromosomal abnormalities as an indicator of minimal residual disease in follow-up samples from the bone marrow (BM), or peripheral blood, of 25 patients with leukemia, lymphoma and myelodysplastic syndromes. Trisomies were detected by interphase FISH with repeat-sequence probes (RSP) or by using metaphase FISH with whole-chromosome paint probes (WCP). Specific translocations were detected using WCP probes. Translocations were observed using metaphase FISH in two patients in uncertain or complete remission (CR), who both later suffered relapse. Five patients with no abnormal cells remained in CR. Four patients with trisomies detected during CR suffered relapse; metaphase FISH detected the trisomy in 0.17-16% of metaphase cells. Five patients for whom the trisomy occurred in 0.034% of cells remained in CR. Trisomic nuclei were observed in 0.27-2.3% of interphase cells, by means of RSPs, in four patients who later suffered relapse. Five patients with trisomic nuclei in 0.061% remained in CR. When two probes were used simultaneously in a sample from one patient, 1% of the residual cells were abnormal. The patient later suffered relapse. In one patient with anaplastic large cell lymphoma, CD30-positive interphase cells were shown to have trisomic chromosome 7 by immunophenotyping and FISH. Our results suggest that metaphase FISH using WCP probes is a sensitive and specific method for detecting minimal residual disease especially in patients with translocations.